tbuckley/cabot-search huggingface dataset:
Abstract 879: Exosomal mRNAs secreted from pancreatic cancer (PC) cell lines might include good candidates of biomarkers of PC patients
Authors: Yuhan Rong, Naoki Okubo, Risa Fukui, Akihiro Suzuki, Motokazu Sato, Motohiko Tokuhisa, Yuma Takeda, Noritoshi Kobayashi, Itaru Endo, Yasushi Ichikawa
Journal: Cancer Research (2023)

Abstract Background: Exosomal mRNAs secreted from cancer cells are regarded as important messengers in communication system between cells. In PC, some exosomal RNAs from patients’ plasma were expected as biomarkers of PC. However, exosomes in the blood of cancer patients are not derived only from cancer cells. Relationship of RNAs produced in cancer cells and those secreted into exosomes is still unclear. In this study, we evaluated relationships between mRNAs in PC cell lines and those of exosomes secreted into supernatant and determined candidates for PC biomarkers from cancer specific exosomal mRNAs. Material and Method: Three PC cell lines (PANC-1, MIAPaCa-2 and Capan-1) were used. Three studies were performed for each cell line. After 48h serum-free culture, the supernatants were collected, and exosomes were isolated by ultracentrifugation. The remaining cells in the culture dish were also collected and mRNAs were extracted. RNA-seq was performed for mRNAs extracted from cell and exosomal RNAs extracted from supernatant. Data was analyzed by R (version 4.2.1). Results: In MIAPaCa-2, expression of cellular mRNAs and corresponding exosomal mRNAs showed strong correlation (R was higher than 0.7). In the other 2 cell lines, they showed moderate correlation (R was higher than 0.5). Then, expression of mRNA in the cells was approximately reflected in those in the exosomes. However, some mRNAs showed high expression in exosome and low expression in the cell. We focused on these mRNAs, and then, performed a differential analysis of the whole raw RNA data by using TCC package of R and found differentially expressed mRNAs. Conclusion: Comparing with data of GEO database showing exosomal mRNA extracted from healthy volunteers, we finally find candidates of cancer specific exosomal mRNAs of PC. Citation Format: Yuhan Rong, Naoki Okubo, Risa Fukui, Akihiro Suzuki, Motokazu Sato, Motohiko Tokuhisa, Yuma Takeda, Noritoshi Kobayashi, Itaru Endo, Yasushi Ichikawa. Exosomal mRNAs secreted from pancreatic cancer (PC) cell lines might include good candidates of biomarkers of PC patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 879.
Abstract 812: Treatment of metastatic cancers using immunotherapeutic cowpea mosaic virus nanoparticles
Authors: Young Hun Chung, Britney A. Volckaert, Nicole F. Steinmetz
Journal: Cancer Research (2023)

Abstract This study investigates the use of an immunotherapeutic plant virus, namely the cowpea mosaic virus (CPMV), that when used prophylactically and therapeutically can protect against metastatic cancer in multiple tumor mouse models. Metastatic cancer continues to be the main cause of death of most cancer patients, and new treatment modalities must be engineered to protect patients from metastatic disease. For instance, peritoneal metastases (PMs) are oftentimes fatal, and patients survive for a median 6 months following diagnosis. PMs are common for colon, ovarian, gastric, appendiceal, and pancreatic cancers. Previously, it was demonstrated that CPMV is a potent in situ vaccine causing tumor shrinkage with abscopal effect and long-term protection observed in tumor mouse models and canine cancer patients. CPMV functions as a toll like receptor (TLR) agonist and acts on innate immune cells to induce tumor cell killing and antigen processing to eventually prime adaptative and tumor-specific immunity. However, metastatic cancers such as PMs are not easily and directly injectable and therefore, we have expanded the ability of CPMV to protect against PMs by engineering targeted CPMV nanoparticles. Data indicates that CPMV can improve survival and slow tumor growth in a murine colon PM model compared to controls and that long-term survivors are further protected from re-challenge indicating tumor specificity. Analysis from current and past studies indicate that CPMV injection into the intraperitoneal space leads to distinct upregulation of immunostimulatory cytokines and recruitment of innate immune cell populations. PMs lead to extreme declines in quality of life of patients, and current treatments can be ineffective in slowing down or reducing tumor development and death - in tackling this problem, the data clearly points to the strong potential for CPMV-mediated therapeutics in the treatment and prophylaxis of PMs. Dr. Steinmetz is a co-founder of and has a financial interest in Mosaic ImmunoEngineering Inc. The other authors have no conflict of interest to declare. Acknowledgments: This work is supported in part through NIH grants R01 CA274640, R01 CA224605, R01 CA253615, CDMRP W81XWH2010742, and the Shaughnessy Family Fund for Nano-ImmunoEngineering (nanoIE at UC San Diego). Citation Format: Young Hun Chung, Britney A. Volckaert, Nicole F. Steinmetz. Treatment of metastatic cancers using immunotherapeutic cowpea mosaic virus nanoparticles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 812.
Abstract 862: Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis of lung adenocarcinoma
Authors: Jorge A. Alfaro-Murillo, Krishna Dasari, Jeffrey P. Townsend
Journal: Cancer Research (2023)

Abstract The somatic evolution of cancer depends on the rate at which new mutations are acquired, as well as the selective pressure acting on them. Further, mutual exclusivity or co-occurrence of mutations suggests that variants can exert antagonistic or synergistic epistatic effects on the selection of new mutations, contributing to a complex landscape of evolutionary trajectories. Estimation of pairwise and higher-order epistatic effects—essential to estimation of the trajectory of likely cancer genotoypes—has remained a challenge. We have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation (flux), dependent on somatic cancer genotype. Coupling the continuous-time Markov chain model with a deconvolution approach provides estimates of underlying mutation rates and selection across the trajectory of oncogenesis. We demonstrate computation of fluxes and selection coefficients in a somatic evolutionary model of lung adenocarcinoma informed by a compilation of samples from multiple data sets including The Cancer Genome Atlas and the AACR Project GENIE. The approach enables inference of the most likely routes of site-specific variant evolution and estimation of the selection strength operating on each step along the route, a key component of what we need to know to develop and implement personalized cancer therapies. Finally, by comparing smoker and nonsmoker tumor cohorts, we reveal and describe distinct evolutionary trajectories, influenced not only by differential mutation, but also by the differential physiological effects that smoking can have on the selective regime of lung tissue. These distinctions disambiguate the physiological and mutational influences of smoking and can inform personalized treatment of the two groups. Citation Format: Jorge A. Alfaro-Murillo, Krishna Dasari, Jeffrey P. Townsend. Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis of lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 862.
Abstract 905: A novel bioluminescent bioassay platform for the discovery and development of engineered T cell therapies for cancer
Authors: Jamison Grailer, Michael Slater, Jim Hartnett, Frank Fan, Mei Cong
Journal: Cancer Research (2023)

Abstract Adoptive transfer of T cells genetically modified to express antigen receptor transgenes has shown promise for the treatment of cancer. Both chimeric antigen receptors (CARs) and transgenic T cell receptors (TCRs) have been used to redirect T cells in preclinical and clinical studies. TCR Therapy (TCR-T) can target essentially any tumor antigen via the major histocompatibility (MHC) system. However, the development of novel tumor antigen specific TCRs is hampered by the lack of easy-to-use model systems and sensitive readouts to facilitate candidate screening and development. Particularly, determination of transgenic TCR activation in primary and immortalized T cells is confounded by the presence of endogenous TCR expression which results in mixed alpha/beta TCR pairings and compression of assay readouts. Herein, we describe the development of a novel cell-based TCR knockout (TCR-KO) reporter assay platform for the development and characterization of novel TCR candidates. CRISPR/Cas9 was used to knockout the endogenous TCR chains in a T cell line that stably expresses a luciferase reporter gene responsive to TCR activation. Reintroduction of a transgenic TCR into the TCR-KO reporter cells results in robust antigen-specific reporter activation compared to parental reporter cells. The further development of CD4/CD8 double-positive and double-negative versions enable low and functional high avidity TCR screening with or without MHC bias. Furthermore, stable TCR-expressing reporter cells generated from TCR-KO reporter cells exhibit sufficient sensitivity and robustness for safety and specificity studies of lead TCR candidates. Together, our data demonstrate that TCR-KO reporter cells can be a useful tool for the discovery, characterization, and deployment of T cell immunotherapy. Citation Format: Jamison Grailer, Michael Slater, Jim Hartnett, Frank Fan, Mei Cong. A novel bioluminescent bioassay platform for the discovery and development of engineered T cell therapies for cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 905.
Abstract 904: Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma
Authors: Tanya Ghosh, Avirup Chakraborty, Linchun Jin, Diana Feier, Aryeh Silver, Maryam Rahman, Catherine Flores, Matthew Sarkisian, Jianping Huang, Duane A. Mitchell, Loic P. Deleyrolle
Journal: Cancer Research (2023)

Abstract Glioblastoma represent a great challenge and current therapies are negligibly effective, with disease recurrence being inevitable. T cell therapy has emerged as a viable treatment for brain malignancies. While promising, the efficacy of this approach is often limited by a complex immunosuppressive tumor microenvironment. These complexities mean that more sophisticated T cell products are required. The brain tumor microenvironment provides local restraints via metabolic competition suppressing antitumor immunity, specifically inhibiting infiltration and effector functions of host and adoptively transferred tumor-reactive T cells. The objective of this project is to test new treatments to reverse immune dysfunction in brain cancer through the regulation of T cell metabolic signaling. We propose that modulating glucose signaling can potentiate T cell anti-tumor activity. The glucose signaling pathway of T cells was modulated through overexpression of glucose transporters and the function of metabolically modified T cells was investigated using murine and human models. We revealed a competition for glucose between T cells and tumor cells, with tumor cells imposing glucose restriction mediating T cell hyporesponsiveness. Overexpression of glucose transporters such as Glut1 and Glut3 enhanced T cell glucose utilization and provided a survival/growth advantage and greater activation, specifically in glucose-restricted conditions. We established that glucose transporter overexpression improves intratumoral infiltration and expansion of adoptively transferred CAR T cells, resulting in improved survival. Our study integrates fundamental concepts of tumor and immune metabolism in the design of immunotherapy and confirms that immunometabolism represents a viable target for new cancer therapy to treat brain tumors. Citation Format: Tanya Ghosh, Avirup Chakraborty, Linchun Jin, Diana Feier, Aryeh Silver, Maryam Rahman, Catherine Flores, Matthew Sarkisian, Jianping Huang, Duane A. Mitchell, Loic P. Deleyrolle. Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 904.
Abstract 5893: Suppression of anti-tumor immunity by the <i>Fusobacterium nucleatum</i> protease fusolisin
Authors: Amjad Shhadeh, Liat Dassa, Jamal Fahoum, Nicole Haj, Reuven Wiener, Ofer Mandelboim, Gilad Bachrach
Journal: Cancer Research (2023)

Abstract Fusobacterium nucleatum is an oral pathogen associated with periodontal disease, preterm births and the exacerbation of colorectal, esophageal, pancreatic, and breast cancers. F. nucleatum was previously found to inhibit killing of cancer cells by natural killer (NK) cells and tumor infiltrating T cells by inducing the NK cells killing-suppressing receptors TIGIT and CEACAM1. In this study, we show that the incubation of F. nucleatum with primary human natural killer (NK) cells causes the cleavage of the activating receptors CD16, NKp44 and NKp46 by fusolisin. Fusolisin is a fusobacterial outer-membrane, auto-transporter, serine protease and to date the only functional protease found in F. nucleatum. We previously showed that fusolisin is essential for fusobacterial growth in culture. High expression of a functional recombinant fusolisin in E. coli was enabled using codon optimization and replacement of the fusolisin's signal peptide with that of the E. coli OmpA. Recombinant fusolisin was found to cleave the same NK-activating receptors degraded by F. nucleatum. Cleavage of these activating receptors by fusolisin inhibited NK cells activity including killing of tumor cells in-vitro and in-vivo. Our results provide a new bacterial protease-dependent mechanism in which tumors colonized by F. nucleatum are protected from NK cells attack by exploiting fusolisin proteolytic activity. Importantly, our previous and current results suggest that fusolisin might serve to target for tumor-colonized fusobacteria. Citation Format: Amjad Shhadeh, Liat Dassa, Jamal Fahoum, Nicole Haj, Reuven Wiener, Ofer Mandelboim, Gilad Bachrach. Suppression of anti-tumor immunity by the Fusobacterium nucleatum protease fusolisin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5893.
Abstract 869: Molecular genetic positioning of small intestine and papilla of Vater carcinomas including clinicopathological classification
Authors: Yukiyasu Okamura, Masanori Nakamura
Journal: Cancer Research (2023)

Abstract Purpose: Small intestine carcinoma (SIC) cases in Japan have recently been treated with chemotherapy according to colorectal carcinoma classification, while papilla of Vater carcinoma (PVC) cases according to cholangiocarcinoma (CHC) classification. However, few research reports support the molecular genetic validity of these therapeutic choices. Here, we investigated the clinicopathological and molecular genetic factors of SIC and PVC. Patients and Methods: We used the data from the Japanese version of The Cancer Genome Atlas (JCGA). Additionally, molecular genetic data on gastric adenocarcinoma (GAD), colorectal adenocarcinoma (CRAD), pancreatic ductal adenocarcinoma (PDAC), and CHC were also referred to. Results: This study consisted of tumor specimens from 12 cases of SIC and three cases of PVC treated from January 2014 to March 2019. Among them, six cases had pancreatic invasion. t-Distributed Stochastic Neighbor Embedding analysis showed that the gene expression pattern of SIC was similar not only to those of GAD and CRAD, but also to that of PDAC in the pancreatic invasion cases. In addition, PVC resembled the GAD, CRAD, and PDAC, rather than the CHC. The molecular genetic characteristics of the six patients with pancreatic invasion were: one had high microsatellite instability (MSI-High), two had a TP53 driver mutation, and three had tumor mutation burden values &amp;lt; 1 mutation/Mb with no driver mutation. Conclusions: The molecular genetics of SIC and PVC suggested that they may be similar to GAD, CRAD, and PDAC. In addition, the data demonstrate that pancreatic invasive cases may be classified into several subtypes using molecular genetic factors. Citation Format: Yukiyasu Okamura, Masanori Nakamura. Molecular genetic positioning of small intestine and papilla of Vater carcinomas including clinicopathological classification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 869.
Abstract 899: Deciphering the benefits of variable delivery routes and molecular armoring to enhance efficacy of MUC1-CAR T-cells in targeting triple-negative breast cancer
Authors: Piril Erler, Hana Cho, Jordan Skinner, Laurent Poirot, Beatriz Aranda-Orgilles
Journal: Cancer Research (2023)

Abstract As immune-therapies continue to develop for solid tumors, the tumor microenviroment (TME) poses many challenges that CAR T-cells need to overcome for efficient tumor cell clearance. Tumor immune evasion mechanisms, presence of immunosuppressive factors and cellular resistance to tumor infiltration are key mechanisms that the TME uses to reduce efficacy of T-cells against the tumor. Therapeutic options for triple negative breast cancer (TNBC) remain limited to date despite it being the most aggressive subtype of breast cancers and carrying the poorest prognosis. Tumor-associated MUC1 antigen is overexpressed in a large number of TNBC patients offering an effective discriminatory target for CAR T-cell therapy. Here, we present innovative strategies exploring alternative delivery routes and purposeful armoring of CAR T-cells to boost efficiency while preserving safety. To maintain anti-tumor CAR T-cell cytotoxic and proliferation in the hostile TME of solid tumors, we developed state-of-the-art multiplexed gene editing using high precision TALEN® technology. With that aim, we armored allogeneic CAR T-cells with specific attributes to release immune inflammatory cytokines and protect from inhibitory effects of the TGFB1 and PD1 pathways. A combination of strategies using allogeneic CAR T-cells with diverse attributes were evaluated against TNBC tumors in various in vivo pre-clinical models. Local CAR T-delivery resulted in effective control of tumor growth and robust antigen specific recognition. Furthermore, we assessed how the delivery route contributes to CAR-T cell distribution. CAR T-cell activity could also be increased systemically upon tumor-specific release of immunostimulatory cytokines without compromising safety. Our results demonstrate not only superior activity of armored MUC1-CAR T-cells resulting in tumor clearance but also in the recovery of normal glands. Thus, innovative strategies can be used to allow CAR T-cell efficiency in the hostile tumor microenvironment while preserving safety. Overall, our pre-clinical results underline the capability of armored allogenic MUC1-CAR T-cells to excel in the immune suppressive tumor micro-environment, suggesting that allogenic MUC1-CAR T-cell therapy could be an effective option in treating relapsed/refractory TNBC patients with limited therapeutic options. Citation Format: Piril Erler, Hana Cho, Jordan Skinner, Laurent Poirot, Beatriz Aranda-Orgilles. Deciphering the benefits of variable delivery routes and molecular armoring to enhance efficacy of MUC1-CAR T-cells in targeting triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 899.
Abstract 87: The role of miro1-mediated mitochondrial positioning in the development and metastasis of breast cancer
Authors: Randi Gravelle, Margaret McCoy, Nathaniel Shannon, Martin Chang, Brian Cunniff
Journal: Cancer Research (2023)

Abstract Miro1 is an outer mitochondrial membrane protein that links mitochondria to motor protein complexes to support subcellular mitochondrial trafficking. Preliminary observations and published work has established that metastatic breast cancer cells have increased expression of Miro1 in comparison to breast cancer cells with low metastatic potential. Furthermore, tumors from breast cancer patients with high Miro1 expression have poorer survival rates compared to patients harboring tumors with low Miro1 expression. This data suggests that Miro1 has a functional role in aggressive breast cancers although this has not been widely studied or confirmed in advanced preclinical models. The objective of our research is to investigate the role of Miro1 in breast cancer tumorigenesis and metastasis. We hypothesize that that Miro1-mediated mitochondrial dynamics support subcellular signaling events driving cell migration, invasion, and tumorigenesis. To examine the function of Miro1 in promoting metastatic phenotypes in vitro, we generated human breast cancer cell lines (MDA-MB-231, MDA-MB-468, T-47d, and MCF7) with Miro1 knockdown using adenoviral shRNA. Knockdown of Miro1 to levels greater than 50% of that in control cells resulted in mitochondria sequestered around the nucleus and reduced cell migration. Additionally, MDA-MB-231 cells with ≥50% Miro1 knockdown resulted in a significant decrease in cell invasion through Matrigel coated membranes in transwell invasion assays. Our research has also uncovered altered phosphorylation of key cell migration and stress-response proteins including vinculin, focal adhesion kinase and ERK ½ when Miro1 is knocked down. To investigate the role of Miro1 in vivo, we generated a novel transgenic mouse model with inducible, tissue specific Miro1 deletion in mammary epithelial cells with concurrent polyomavirus middle T-antigen oncogene activation. We found that when breast cancer formation is induced utilizing the transgenic middle-T antigen system, our control mice form tumors at all mammary gland sites and have metastasis to the lungs. Conversely, mice with concurrent Miro1 deletion and middle T- antigen activation fail to develop tumors. This data suggests that Miro1 has a functional role in both mammary tumor onset and tumor cell migration and invasion, providing a possible new biomarker of tumor status and pathway for therapeutic intervention. Citation Format: Randi Gravelle, Margaret McCoy, Nathaniel Shannon, Martin Chang, Brian Cunniff. The role of miro1-mediated mitochondrial positioning in the development and metastasis of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 87.